diff --git a/stim/cuda/branch_detection.cuh b/stim/cuda/branch_detection.cuh
index 61105e0..9adf987 100644
--- a/stim/cuda/branch_detection.cuh
+++ b/stim/cuda/branch_detection.cuh
@@ -7,7 +7,7 @@
 #include <stim/cuda/cuda_texture.cuh>
 #include <stim/cuda/filter.cuh>
 typedef unsigned int uint;
-typedef unsigned int uchar;
+//typedef unsigned int uchar;
 
 
 std::vector< stim::vec<float> >
diff --git a/stim/cuda/spider_cost.cuh b/stim/cuda/spider_cost.cuh
index d35ef75..10d7f5f 100644
--- a/stim/cuda/spider_cost.cuh
+++ b/stim/cuda/spider_cost.cuh
@@ -3,7 +3,7 @@
 
 #include <assert.h>
 #include <cuda.h>
-#include <cuda_runtime.h>
+//#include <cuda_runtime.h>
 #include <stdio.h>
 #include <stim/visualization/colormap.h>
 #include <sstream>
diff --git a/stim/grids/image_stack.h b/stim/grids/image_stack.h
index 0f99409..afb9a12 100644
--- a/stim/grids/image_stack.h
+++ b/stim/grids/image_stack.h
@@ -68,7 +68,7 @@ public:
 			stim::image<T> I(file_list[i].str());
 
 			//retrieve the interlaced data from the image - store it in the grid
-			I.data_interleaved(&ptr[ i * R[0] * R[1] * R[2] ]);
+			I.get_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ]);
 			
 		}
 	}
diff --git a/stim/image/image.h b/stim/image/image.h
index 9cb985d..d101ec4 100644
--- a/stim/image/image.h
+++ b/stim/image/image.h
@@ -148,7 +148,7 @@ public:
 		if(C() == 1)
 			memcpy(buffer, img, bytes());
 		else if(C() == 3)
-			data_interleaved_bgr(buffer);
+			get_interleaved_bgr(buffer);
 		cv::Mat cvImage((int)Y(), (int)X(), cv_type(), buffer);
 		cv::imwrite(filename, cvImage);
 	}
@@ -170,7 +170,7 @@ public:
 		}
 	}
 
-	void data_interleaved_bgr(T* data){
+	void get_interleaved_bgr(T* data){
 
 		//for each channel
 		for(size_t y = 0; y < Y(); y++){
@@ -182,6 +182,11 @@ public:
 		}
 	}
 
+	void get_interleaved_rgb(T* data){
+		memcpy(data, img, bytes());
+	}
+
+
 	image<T> channel(size_t c){
 
 		//create a new image
diff --git a/stim/math/circle.h b/stim/math/circle.h
index 852ff9d..874b292 100644
--- a/stim/math/circle.h
+++ b/stim/math/circle.h
@@ -175,5 +175,4 @@ public:
 
 };
 }
->>>>>>> origin/Master_Clone_W_Branch
 #endif
diff --git a/stim/parser/filename.h b/stim/parser/filename.h
index 613bdb8..f33a492 100644
--- a/stim/parser/filename.h
+++ b/stim/parser/filename.h
@@ -22,6 +22,9 @@
 #include <iostream>
 
 #include "../parser/parser.h"
+#ifdef BOOST_PRECOMPILED
+#include <boost/filesystem.hpp>
+#endif
 namespace stim{
 
 //filename class designed to work with both Windows and Unix
@@ -234,8 +237,40 @@ public:
 		}
 		return file_list;
 #else
-	std::cout<<"File lists aren't currently supported on Unix/Linux systems."<<std::endl;
-	exit(1);
+
+		boost::filesystem::path p(dir());	//create a path from the current filename
+		std::vector<stim::filename> file_list;
+		if(boost::filesystem::exists(p)){
+			if(boost::filesystem::is_directory(p)){
+				typedef std::vector<boost::filesystem::path> vec;             // store paths,
+				vec v;                                // so we can sort them later
+				std::copy(boost::filesystem::directory_iterator(p), boost::filesystem::directory_iterator(), back_inserter(v));
+				std::sort(v.begin(), v.end());             // sort, since directory iteration
+				  // is not ordered on some file systems
+				//compare file names to the current template (look for wild cards)
+				for (vec::const_iterator it(v.begin()), it_end(v.end()); it != it_end; ++it)
+				{
+					//if the filename is a wild card *or* it matches the read file name
+					if( prefix == "*" || prefix == (*it).filename().stem().string()){
+						//if the extension is a wild card *or* it matches the read file extension
+						if( ext == "*" || "." + ext == (*it).filename().extension().string()){
+							file_list.push_back((*it).string());	//include it in the final list
+						}
+
+					}
+
+
+
+				}
+
+			}
+
+		}
+		return file_list;
+
+
+//	std::cout<<"File lists aren't currently supported on Unix/Linux systems."<<std::endl;
+//	exit(1);
 #endif
 	}
 	//**************************************************************************************************
diff --git a/stim/visualization/cylinder.h b/stim/visualization/cylinder.h
index 1dfbc5b..f203a77 100644
--- a/stim/visualization/cylinder.h
+++ b/stim/visualization/cylinder.h
@@ -164,7 +164,7 @@ class cylinder
 		///Returns the number of points on the cylinder centerline
 
 		unsigned int size(){
-			return pos.size();
+			return e.size();
 		}
 
 
@@ -231,7 +231,7 @@ class cylinder
 		/// Adds a new magnitude value to all points
 		/// @param m is the starting value for the new magnitude
 		void add_mag(T m = 0){
-			for(unsigned int p = 0; p < pos.size(); p++)
+			for(unsigned int p = 0; p < e.size(); p++)
 				mags[p].push_back(m);
 		}
 
@@ -317,7 +317,7 @@ class cylinder
 			T len = L[0];						//allocate space for the segment length
 
 			//for every consecutive point in the cylinder
-			for(unsigned p = 1; p < pos.size(); p++){
+			for(unsigned p = 1; p < e.size(); p++){
 
 				//p1 = pos[p];							//get the position and magnitude for the next point
 				m1 = mags[p][m];
@@ -347,7 +347,7 @@ class cylinder
 
 			std::vector< vec<T> > result;
 
-			vec<T> p0 = e[i].P;								//initialize p0 to the first point on the centerline
+			vec<T> p0 = e[0].P;								//initialize p0 to the first point on the centerline
 			vec<T> p1;
 			unsigned N = size();							//number of points in the current centerline
 
diff --git a/stim/visualization/obj.h b/stim/visualization/obj.h
index e625f55..09e8a68 100644
--- a/stim/visualization/obj.h
+++ b/stim/visualization/obj.h
@@ -158,6 +158,7 @@ protected:
 		using std::vector<triplet>::size;
 		using std::vector<triplet>::at;
 		using std::vector<triplet>::push_back;
+		using std::vector<triplet>::resize;
 
 		geometry(){}
 
--
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